This paper presents the scientific study of the effectiveness and action principle of head meridian acupoint massage by applying the grey data model analysis approach. First, the head massage procedure for massaging the important head meridian acupuncture points including Taiyang, Fengfu, Tianzhu, Fengqi, and Jianjing is formulated in a standard manner. Second, the status of the autonomic nervous system of each subject is evaluated by using the heart rate variability analyzer before and after the head massage following four weeks. Afterward, the physiological factors of autonomic nerves are quantitatively analyzed by using the grey data modeling theory. The grey data analysis can point out that the status of autonomic nervous system is greatly improved after the massage. The order change of the grey relationship weighting of physiological factors shows the action principle of the sympathetic and parasympathetic nerves when performing head massage. In other words, the grey data model is able to distinguish the detailed interaction of the autonomic nervous system and the head meridian acupoint massage. Thus, the stress relaxing effect of massaging head meridian acupoints is proved, which is lacked in literature. The results can be a reference principle for massage health care in practice.